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Revert to sampling all data (using the minimum number of non-overlapping samples) #19

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Jan 16, 2023
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Revert to sampling all data (using the minimum number of non-overlapping samples) #19

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276c54a
Try a different sampling approach
arm61 Jan 3, 2023
51f5fcd
Implementing everything for running the paper/
arm61 Jan 6, 2023
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6 changes: 3 additions & 3 deletions docs/source/arrhenius_t.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@
"id": "c204d962-a8f8-4989-9d84-e9a6ae52730f",
"metadata": {},
"source": [
"The list of diffusion coefficient objects (which are `uravu.distribution.Distribution` type objects) and array of temperatures can then be passed to the `kinisi.arrhenius.StandardArrhenius` class. "
"The list of diffusion coefficient objects (which are `uravu.distribution.Distribution` type objects) and array of temperatures can then be passed to the `kinisi.arrhenius.StandardArrhenius` class, where we use the `bounds` keyword argument to give a minimum and maximum value for the activation energy and preexponential factor."
]
},
{
Expand All @@ -122,7 +122,7 @@
"metadata": {},
"outputs": [],
"source": [
"s = StandardArrhenius(temperatures, D)"
"s = StandardArrhenius(temperatures, D, bounds=((0.01, 0.2), (1e-5, 1e-1)))"
]
},
{
Expand All @@ -140,7 +140,7 @@
"metadata": {},
"outputs": [],
"source": [
"s.max_likelihood('diff_evo')"
"s.max_likelihood('mini')"
]
},
{
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5 changes: 3 additions & 2 deletions docs/source/vasp_d.ipynb
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Expand Up @@ -125,7 +125,8 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"It appears that the non-Gaussian parameter does not accurately predict the start of the diffusive regime for this example, so we will set the start of the diffusive regime to be 4 ps using the keyword argument of `dt_skip=4`. \n",
"It appears that the non-Gaussian parameter does okay at predicting the of the diffusive regime for this example (it is slightly underestimated), therefore we will set the `use_ngp` keyword argument to `True`. \n",
"If the non-Gaussian parameter gave an incorrect value, the start of the diffusive regim could be set to, say, 4 ps using the keyword argument of `dt_skip=4`. \n",
"The `d_params` dictionary defines parameters about the diffusion estimation, documented in the [diffusion module](https://kinisi.readthedocs.io/en/latest/diffusion.html#kinisi.diffusion.MSDBootstrap). "
]
},
Expand All @@ -135,7 +136,7 @@
"metadata": {},
"outputs": [],
"source": [
"d_params = {'dt_skip': 4}"
"d_params = {'use_ngp': True}"
]
},
{
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